mantel {vegan} | R Documentation |
Function mantel
finds the Mantel statistic as a matrix
correlation between two dissimilarity matrices, and function
mantel.partial
finds the partial Mantel statistic as the
partial matrix correlation between three dissimilarity matricies. The
significance of the statistic is evaluated by permuting rows and
columns of the first dissimilarity matrix.
mantel(xdis, ydis, method="pearson", permutations=999, strata) mantel.partial(xdis, ydis, zdis, method = "pearson", permutations = 999, strata)
xdis, ydis, zdis |
Dissimilarity matrices or a dist objects. |
method |
Correlation method, as accepted by cor :
"pearson" , "spearman" or "kendall" . |
permutations |
Number of permutations in assessing significance. |
strata |
An integer vector or factor specifying the strata for permutation. If supplied, observations are permuted only within the specified strata. |
Mantel statistic is simply a correlation between entries of two dissimilarity matrices (some use cross products, but these are linearly related). However, the significance cannot be directly assessed, because there are N(N-1)/2 entries for just N observations. Mantel developed asymptotic test, but here we use permutations of N rows and columns of dissimilarity matrix.
Partial Mantel statistic uses partial correlation
conditioned on the third matrix. Only the first matrix is permuted so
that the correlation structure between second and first matrices is
kept constant. Although mantel.partial
silently accepts other
methods than "pearson"
, partial correlations will probably be
wrong with other methods.
The function uses cor
, which should accept
alternatives pearson
for product moment correlations and
spearman
or kendall
for rank correlations.
The function returns a list of class mantel
with following
components:
Call |
Function call. |
method |
Correlation method used, as returned by
cor.test . |
statistic |
The Mantel statistic. |
signif |
Empirical significance level from permutations. |
perm |
A vector of permuted values. |
permutations |
Number of permutations. |
Legendre & Legendre (1998) say that partial Mantel correlations often are difficult to interpet.
Jari Oksanen
The test is due to Mantel, of course, but the current implementation is based on Legendre and Legendre.
Legendre, P. and Legendre, L. (1998) Numerical Ecology. 2nd English Edition. Elsevier.
cor
for correlation coefficients,
protest
(``Procrustes test'') for an alternative with
ordination diagrams, anosim
and mrpp
for comparing dissimilarities against
classification. For dissimilarity matrices, see vegdist
or dist
. See bioenv
for selecting
environmental variables.
## Is vegetation related to environment? data(varespec) data(varechem) veg.dist <- vegdist(varespec) # Bray-Curtis env.dist <- vegdist(scale(varechem), "euclid") mantel(veg.dist, env.dist) mantel(veg.dist, env.dist, method="spear")